GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Leptospirillum ferrooxidans C2-3

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_232502519.1 LFE_RS09120 ATP-binding cassette domain-containing protein

Query= TCDB::G3LHY8
         (358 letters)



>NCBI__GCF_000284315.1:WP_232502519.1
          Length = 588

 Score = 91.3 bits (225), Expect = 6e-23
 Identities = 70/205 (34%), Positives = 106/205 (51%), Gaps = 9/205 (4%)

Query: 24  LERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQKR-NVAMVYQQF 82
           L++G++  L+GP  AGKT+LMRL++GL  P GG I   G D +  P+  + ++  + Q+F
Sbjct: 37  LKKGSITGLIGPDGAGKTTLMRLLSGLLWPDGGDIRIMGNDPSKAPLSVQGSLGYMPQKF 96

Query: 83  INYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLT---PYLDRTPLNLSGGQQQR 139
             Y  L+V  N+     + G      DR     A LL +T   P+  R    LSGG +Q+
Sbjct: 97  GLYEDLSVQENLDLYANLQGVPK---DRRKELYAPLLSMTGLSPFQKRLAGQLSGGMKQK 153

Query: 140 TALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEPSEALLLG 199
             +A +LV    ++L+DEP   +D   R EL E L K+ ++SGA    +T+   EA    
Sbjct: 154 LGVACSLVHQPPILLLDEPTVGVDPVSRRELWEILRKLVSESGATLFVSTSYLDEAERC- 212

Query: 200 GNTATLNQGRVTQFGPTIEVYRRPV 224
                L  G+V   GP  E +R+ V
Sbjct: 213 DEILILYNGKVLGSGPP-ESFRKEV 236



 Score = 73.2 bits (178), Expect = 2e-17
 Identities = 46/147 (31%), Positives = 75/147 (51%), Gaps = 1/147 (0%)

Query: 24  LERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQKRN-VAMVYQQF 82
           +++G +  LLG   AGKT+  R++AGL  PT G +   G DV  +  Q R  +  + Q+F
Sbjct: 364 VKKGEVFGLLGANGAGKTTTFRMLAGLLEPTAGKLIVAGEDVRKVAAQARGKIGYMAQKF 423

Query: 83  INYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNLSGGQQQRTAL 142
             Y  LTV+ N+       G        +++ +    +L PY + +   L  G +QR AL
Sbjct: 424 SLYSQLTVFQNLIFYSSAYGLSGTLQKEKIQDSLNFFELEPYKNVSSGILPLGFRQRLAL 483

Query: 143 ARALVKNASLVLMDEPLANLDYKLREE 169
           + AL+   S++ +DEP + +D   R E
Sbjct: 484 SCALIHEPSILFLDEPTSGVDPNARRE 510


Lambda     K      H
   0.319    0.136    0.392 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 495
Number of extensions: 28
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 358
Length of database: 588
Length adjustment: 33
Effective length of query: 325
Effective length of database: 555
Effective search space:   180375
Effective search space used:   180375
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory